Contacts of the helix formed by residues 307 - 319 (chain A) in PDB entry 3KSA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ALA* 4.7 18.4 - - + -
283A GLY* 5.2 2.7 - - - +
305A ASP* 2.6 19.5 + - + +
306A ALA* 1.3 66.8 - - - +
308A THR* 1.3 62.7 + - - +
309A GLU* 3.2 3.6 - - - -
310A LEU* 2.9 18.4 + - + -
311A VAL* 2.9 20.2 + - + +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLN 6.2 1.6 - - - +
254A ILE* 4.9 5.4 - - - +
302A LEU* 3.8 30.5 - - + +
306A ALA* 2.5 49.9 + - + +
307A ASN* 1.3 70.5 - - - +
309A GLU* 1.3 62.8 + - - +
311A VAL* 3.0 2.8 + - - +
312A LEU* 2.7 37.7 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ALA 4.7 0.2 + - - -
307A ASN 3.1 1.4 + - - -
308A THR* 1.3 85.6 + - - +
310A LEU* 1.3 58.1 + - - +
312A LEU* 3.9 16.2 - - - +
313A ASN* 2.9 33.1 + - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 5.0 4.1 - - + +
282A ALA* 6.4 0.7 - - + -
307A ASN* 2.9 20.7 + - + +
309A GLU* 1.3 78.4 - - - +
311A VAL* 1.3 57.7 + - - +
313A ASN* 4.0 4.5 - - - +
314A TYR* 2.9 30.8 + - - +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ILE* 5.3 2.5 - - + -
281A VAL* 4.7 20.5 - - + +
282A ALA* 6.3 0.7 - - + -
283A GLY* 5.3 9.0 - - - +
284A ILE* 5.4 2.5 - - - +
302A LEU* 4.6 15.9 - - + -
307A ASN* 2.9 13.1 + - + +
308A THR* 3.4 12.8 - - - +
310A LEU* 1.3 73.7 - - - +
312A LEU* 1.3 59.9 + - - +
314A TYR* 3.4 6.0 + - - +
315A LEU* 2.9 36.2 + - + +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 4.5 18.6 - - - -
254A ILE* 4.5 27.7 - - + +
308A THR 2.7 20.2 + - - +
309A GLU* 3.9 17.5 - - - +
311A VAL* 1.3 69.5 - - - +
313A ASN* 1.3 66.5 + - - +
315A LEU* 3.1 10.5 + - + +
316A PHE* 2.9 60.7 + - + +
321A LEU* 5.3 4.5 - - + -
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A GLU* 2.9 21.7 + - - +
310A LEU* 4.0 5.6 - - - +
312A LEU* 1.3 75.9 - - - +
314A TYR* 1.3 63.2 + - - +
316A PHE* 3.6 12.9 + - - +
317A LYS* 3.4 18.4 + - - +
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Residues in contact with TYR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 3.9 22.1 - - + +
280A LYS* 3.6 27.0 + - + +
281A VAL* 3.6 38.6 - - + -
310A LEU 2.9 20.3 + - - +
311A VAL 3.5 3.4 - - - +
313A ASN* 1.3 73.7 - - - +
315A LEU* 1.3 73.4 + - + +
317A LYS* 2.9 9.9 + - + +
318A TYR* 2.8 50.9 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ILE* 5.2 4.9 - - + -
272A ILE* 4.1 21.1 - - + -
275A VAL* 4.5 22.0 - - + -
281A VAL* 6.4 0.7 - - + -
300A ILE* 3.3 37.0 - - + -
311A VAL* 2.9 23.6 + - + +
312A LEU* 3.5 13.7 - - + +
314A TYR* 1.3 76.1 - - + +
316A PHE* 1.3 64.5 + - - +
319A THR* 2.8 53.3 + - + +
321A LEU* 4.2 14.8 - - + -
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ARG* 4.5 10.5 - - + -
240A SER* 3.8 34.1 - - - -
242A THR* 5.2 6.5 - - - -
312A LEU* 2.9 47.6 + - + -
313A ASN* 3.7 13.2 - - - +
315A LEU* 1.3 75.9 - - - +
317A LYS* 1.3 65.0 + - - +
319A THR 3.0 15.4 - - - +
321A LEU* 3.9 15.3 - - + -
322A GLN* 3.4 38.6 - - + +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ASN 3.4 8.8 + - - +
314A TYR* 2.9 17.3 + - + +
316A PHE* 1.3 79.7 - - - +
318A TYR* 1.3 62.9 + - + +
319A THR 3.4 3.3 + - - +
322A GLN 5.1 0.5 - - - +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LYS* 2.8 27.0 + - - +
275A VAL* 5.2 1.3 - - + -
314A TYR* 2.8 58.0 + - + +
317A LYS* 1.3 73.6 - - + +
319A THR* 1.3 54.1 + - + +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU* 4.3 7.6 - - - +
271A LYS* 3.5 35.2 - - - +
272A ILE* 4.4 6.3 - - + +
275A VAL* 4.4 8.3 - - + -
315A LEU* 2.8 45.0 + - + +
316A PHE 3.0 18.5 - - - +
317A LYS 3.8 2.6 - - - +
318A TYR* 1.3 77.7 - - + +
320A ASP* 1.3 61.3 + - - +
321A LEU* 3.1 20.5 + - - +
322A GLN 3.3 5.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il